Apolipoprotein E (apoE) is a 299 amino acid (~34 kD) protein that plays a central role in lipid transport and metabolism. Unlike apoE3 and apoE2, apoE4 is an established risk factor for Alzheimer's disease (AD). However, the molecular basis of these isoform-specific effects is largely unknown and, most importantly, has not been explored systematically in terms of structure and function. Most attention has been focused on the influence of apoE on A[unreadable] peptide processing in the brain. Specific Aims. Aim 1: Identify the initiation of beta structure in apoE4. Aim 2: Characterize the interaction of apoE isoforms with the A[unreadable] peptide. These aims will illuminate the most important details needed for achieving a mechanistic understanding of how apoE4 participates in AD and neurodegeneration in general. Guided by our (including collaborators) expertise on the functional system, we have the experience and technology to uniquely contribute to this problem by applying the structural biology tools most likely to uncover the basis for the apoE isoform effect in AD. These tools include fluorescence spectroscopy, electron microscopy, surface plasmon resonance, and FTIR spectroscopy, though our primary method will utilize electron paramagnetic (EPR) spectroscopy of site-directed spin labels. Significance. Because of the ability of EPR to report on local structure and spatial relationships from the sample in solution, this work may translate into an effective tool for drug candidate screening. Possibilities include use of spin-labeled side chains to evaluate beta-strand blockers designed to target an identified domain or charged chemical chaperones that stabilize a labile region within apoE. Since apoE3 may also experience destabilized conformations, though at a much lower frequency, such treatments may be helpful in slowing the progression of AD in E3 carriers as well.